ReadSamfile: Read a "SAM file", discarding some reads that cannot be...

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

Description

Read a "SAM file", discarding some reads that cannot be interpreted for our purposes.

Usage

ReadSamfile(filename)

Arguments

filename

The name of the SAM file to read.

Details

SAM stands for "Sequence Alignment Map", a text file that represents aligned next-generation sequencing reads (https://en.wikipedia.org/wiki/SAM_(file_format)). Only keep reads that satisfy certain conditions:

• Mate pair maps to same chromosome

• Mapping quality >= 30

• "FLAG" < 256 (see info on the return value element reads.with.bad.FLAG, below).

• The CIGAR string is only \d+M (one or more digits followed M, and nothing else before or after). This means there are no insertions or deletions in the read versus the reference and there is no soft clipping. Insertions or deletions or clipping shift the read within the SAM file, after which this function cannot keep track of the DBS location.

Value

A a list with the elements:

• good.reads, data.frame with with column names for the first 11 columns as specified in https://en.wikipedia.org/wiki/SAM_(file_format) with one row per read. The result contains only the reads that meet certain conditions.

• total.depth, the initial depth including "bad" reads

• reads.with.bad.FLAG. These are reads with FLAG >= 256, which marks reads that (i) are "not primary alignment" (ii) failed vendor QC (iii) are PCR or optical duplicates (iv) are supplementary alignments (e.g. split, split /inverted read). See https://broadinstitute.github.io/picard/explain-flags.html

• reads.with.bad.CIGAR, reads with CIGAR string that indicates an indel in the read or clipping.

• reads.with.bad.MAPQ, reads with MAPQ < 30.

• reads.with.bad.Mate_CHROM, reads with a mate on a different chromosome.

steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.